Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz

The dynamics of water surrounding a solute is of fundamental importance in chemistry and biology. The properties of water molecules near the surface of a bio-molecule have been the subject of numerous, sometimes controversial experimental and theoretical studies, with some suggesting the existence of rather rigid water structures around carbohydrates and proteins [Pal, S. K., Peon, J., Bagchi, B. & Zewail A. H. (2002) J. Phys. Chem. B 106, 12376–12395]. Hydrogen bond rearrangement in water occurs on the picosecond time scale, so relevant experiments must access these times. Here, we show that terahertz spectroscopy can directly investigate hydration layers. By a precise measurement of absorption coefficients between 2.3 THz and 2.9 THz we could determine the size and the characteristics of the hydration shell. The hydration layer around a carbohydrate (lactose) is determined to extend to 5.13 ± 0.24 A from the surface corresponding to ≈123 water molecules beyond the first solvation shell. Accompanying molecular modeling calculations support this result and provide a microscopic visualization. Terahertz spectroscopy is shown to probe the collective modes in the water network. The observed increase of the terahertz absorption of the water in the hydration layer is explained in terms of coherent oscillations of the hydration water and solute. Simulations also reveal a slowing down of the hydrogen bond rearrangement dynamics for water molecules near lactose, which occur on the picosecond time scale. The present study demonstrates that terahertz spectroscopy is a sensitive tool to detect solute-induced changes in the water network.

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Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm(-1) range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules.

http://iopscience.iop.org/article/10.1088/0031-9155/47/21/318/pdf

THz time domain spectroscopy of biomolecular conformational modes

Terahertz (THz) spectroscopic investigations of condensed-phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the binding force constants and anharmonic character of the force fields, properties necessary to improve predictability but not readily obtainable using any other method. These studies have provided benchmark vibrational data on extended periodic structures for direct comparisons with classical (CHARMm) and quantum chemical (density functional theory) theories. For the larger amorphous and/or aqueous phase samples, the THz modes form a continuum-like absorption that arises because of the full accessibility to conformational space and/or the rapid time scale for inter-conversion in these environments. Despite severe absorption by liquid water, detailed investigations have uncovered the photo- and hydration-induced conformational flexibility of proteins, the solvent shell depth of the water/biomolecule boundary layers and the solvent reorientation dynamics occurring in these interfacial layers that occur on sub-picosecond time scales. As such, THz spectroscopy has enhanced and extended the accessibility to intermolecular forces, length- and timescales important in biological structure and activity.

/pdf/applications-of-terahertz-spectroscopy-in-biosystems-503vyxhk6f.pdf

Applications of Terahertz Spectroscopy in Biosystems

Terahertz (THz) radiation occupies that region of the electromagnetic (EM) spectrum between approximately 03 and 20 THz Recent advances in methods of producing THz radiation have stimulated interest in studying the interaction between radiation and biological molecules and tissue Given that the photon energies associated with this region of the spectrum are 20 x 10(-22) to 13 x 10(-20) J, an analysis of the interactions requires an understanding of the permittivity and conductivity of the medium (which describe the bulk motions of the molecules) and the possible transitions between the molecular energy levels This paper reviews current understanding of the interactions between THz radiation and biological molecules, cells and tissues At frequencies below approximately 6 THz the interaction may be understood as a classical EM wave interaction (using the parameters of permittivity and conductivity), whereas at higher frequencies transitions between different molecular vibrational and rotational energy levels become increasingly important and are more readily understood using a quantum-mechanical framework The latter is of particular interest in using THz to probe transitions between different vibrational modes of deoxyribonucleic acid Much additional experimental work is required in order to fully understand the interactions between THz radiation and biological molecules and tissue

https://iopscience.iop.org/article/10.1088/0031-9155/46/9/201/pdf

The interaction between Terahertz radiation and biological tissue

Far-infrared measurements, between 3 and 450 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$, of absorption spectra of highly oriented films of Li-DNA and Na-DNA in the temperature range 5\char21{}300 K are reported. Five low-frequency infrared-active vibrational modes are observed. The lowest infrared-active mode at 45 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ for Li-DNA and 41 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ for Na-DNA, as observed for the first time, is found to soften upon sample hydration. Studies of the hydration-induced absorption at the low-frequency end of the spectrum also show a pronounced absorption band at about 10 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ that is attributed to relaxation processes. Based on a simple lattice-dynamics model, the description of low-lying vibrational modes of DNA is presented. Eigenvectors of the lowest infrared-active and Raman-active modes are calculated. In addition, the model semiquantitatively describes the influence of hydration on mode frequencies.

A Rupprecht

Papers

Far-infrared spectroscopy on oriented films of dry and hydrated DNA